Graft hypertrophy represents a characteristic complication following autologous chondrocyte implantation (ACI) for treatment of cartilage defects. Although some epidemiological data suggest that incidence is associated with first-generation ACI using autologous chondrocyte implantation, it has also been reported in other technical modifications of ACI using different biomaterials. Nevertheless, it has not been described in autologous, non-periosteum, implant-free associated ACI. In addition, little is known about histological and T2-relaxation appearance of graft hypertrophy. The present case report provides a rare case of extensive graft hypertrophy following ACI using an autologous spheres technique with clinical progression over time. Detailed clinical, MR tomographic and histological evaluation has been performed, which demonstrates a high quality of repair tissue within the hypertrophic as well as non-hypertrophic transplanted areas of the repair tissue. No expression of collagen type X (a sign of chondrocyte hypertrophy), only slight changes of the subchondral bone and a nearly normal cell-matrix ratio suggest that tissue within the hypertrophic area does not significantly differ from intact and high-quality repair tissue and therefore seems not to cause graft hypertrophy. This is in contrast to the assumption that histological hypertrophy might cause or contribute to an overwhelming growth of the repair tissue within the transplantation site. Data presented in this manuscript might contribute to further explain the etiology of graft hypertrophy following ACI.